About the contributors
Roman Affentranger, having obtained his PhD on the development of a novel Hamiltonian Replica Exchange protocol for protein molecular dynamics simulations in 2006 from the Federal Institute of Technology (ETH) in Zurich, Switzerland, worked for three years as postdoctoral scientist for the Group of Computational Biology and Proteomics (Prof. Dr X Daura) at the Institute of Biotechnology and Biomedicine of the Autonomous University of Barcelona, Spain. In 2010, he joined Douglas Connect (Switzerland) as Research Activity Coordinator, where he worked on the EU FP7 projects OpenTox and SYNERGY. At Douglas Connect, Roman Affentranger is currently involved in the scientific coordination and project management of ToxBank, in particular in the setup of project communication resources, the organisation and facilitation of both ToxBank-internal and cross-project working group meetings, the planning of project meetings and workshops, and in dissemination and reporting activities.
Laurent Alquier is currently Project Lead in the Pharma R&D Informatics Center of Excellence at Johnson & Johnson Pharmaceuticals R&D, L.L.C. Laurent has a PhD in optimisation techniques for Pattern Recognition and also holds an engineering degree in Computer Science. Since he joined J&J in 1999, Laurent has been involved in projects across the spectrum of drug discovery applications, from developing chemo-informatics data visualisations to improving compounds logistics processes. His current research interests are focused on using semantic data integration, text mining and knowledge-sharing tools to improve translational informatics.
Teresa Attwood is a Professor of Bioinformatics, with interests in protein sequence analysis that have led to the development of various databases (e.g. PRINTS, InterPro, CADRE) and software tools (e.g. CINEMA, Utopia). Recently, her interests have extended to linking research data with scholarly publications, in order to bring static documents to ‘life’.
Erik Bakke is a Senior Software Engineer at Entagen and works out of the Minneapolis, MN office. He began his career in 2008 working extensively with enterprise Java projects. Coupling that experience with a history of building web-based applications, Erik embraced the Groovy/ Grails framework. His interests include rich, usable interfaces and emerging semantic technologies. He maintains a connection to the next generation of engineers by volunteering as mathematics tutor for K-12 students.
Colin Batchelor is a Senior Informatics Analyst at the Royal Society of Chemistry, Cambridge, UK. A member of the ChemSpider team, he is working on natural language processing for scientific publishing and is a contributor to the InChI and Sequence Ontology projects. His DPhil (physical and theoretical chemistry) is on molecular Rydberg dynamics.
Michael R. Berthold, after receiving his PhD from Karlsruhe University, Germany, spent over seven years in the US, among others at Carnegie Mellon University, Intel Corporation, the University of California at Berkeley and – most recently – as director of an industrial think-tank in South San Francisco. Since August 2003 he holds the Nycomed-Chair for Bioinformatics and Information Mining at Konstanz University, Germany, where his research focuses on using machine-learning methods for the interactive analysis of large information repositories in the life sciences. Most of the research results are made available to the public via the open source data mining platform KNIME. In 2008, he co-founded KNIME. com AG, located in Zurich, Switzerland. KNIME.com offers consulting and training for the KNIME platform in addition to an increasing range of enterprise products. He is a past President of the North American Fuzzy Information Processing Society, Associate Editor of several journals and the President of the IEEE System, Man, and Cybernetics Society. He has been involved in the organisation of various conferences, most notably the IDA-series of symposia on Intelligent Data Analysis and the conference series on Computational Life Science. Together with David Hand he co-edited the successful textbook Intelligent Data Analysis: An Introduction, which has recently appeared in a completely revised, second edition. He is also co-author of the brand-new Guide to Intelligent Data Analysis (Springer Verlag), which appeared in summer 2010.
Erhan Bilal is a Postdoctoral Researcher at the Computational Biology Center at IBM T.J. Watson Research Center. He received his PhD in Computational Biology from Rutgers University, USA. His research interests include cancer genomics, machine-learning and data mining.
Ola Bildtsen is a Senior Software Engineer at Entagen and works out of the Minneapolis, MN office. He has a strong background in rich UI technologies, particularly Adobe’s Flash/Flex frameworks and also has extensive experience with Java and Groovy/Grails building web-based applications. Ola has been working with Java since 1996, and has been in a technical leadership role for the past seven years – the last four of those focused in the Groovy/Grails space. He has a strong background in Java web security and is the author of a Grails security plug-in (Stark Security). Ola holds a BA in Computer Science from Amherst College, and a MS in Software Engineering from the University of Minnesota.
Christopher Bouton received his BA in Neuroscience (Magna Cum Laude) from Amherst College in 1996 and his PhD in Molecular Neurobiology from Johns Hopkins University in 2001. Between 2001 and 2004, Dr Bouton worked as a computational biologist at LION Bioscience Research Inc. and Aveo Pharmaceuticals, leading the microarray data analysis functions at both companies. In 2004 he accepted the position of Head of Integrative Data Mining for Pfizer and led a group of PhD-level scientists conducting research in the areas of computational biology, systems biology, knowledge engineering, software development, machine-learning and large-scale ‘omics data analysis. While at Pfizer, Dr Bouton conceived of and implemented an organisation-wide wiki called Pfizerpedia for which he won the prestigious 2007 William E. Upjohn Award in Innovation. In 2008 Dr Bouton assumed the position of CEO at Entagen (http://www.entagen.com). a biotechnology company that provides computational research, analysis and custom software development services for biomedical organisations. Dr Bouton is an author on over a dozen scientific papers and book chapters and his work has been covered in a number of industry news articles.
Nick Brown is currently an Associate Director in the Innovative Medicines group in New Opportunities at AstraZeneca. New Opportunities is a fully virtualised R&D unit that brings new medicines to patients in disease areas where AstraZeneca is not currently conducting research. His main role is as an informatics leader, working collaboratively to build innovative information systems to seek out new collaborators and academics, access breaking science and identify potential new drug repositioning opportunities. He originally received his degree in Genetics from York University and subsequently went on to receive his masters in Bioinformatics. He joined AstraZeneca as a bioinformatician in 2001, developing scientific software and automating toxicogenomic analyses. In 2004 he moved to the Advanced Science & Technology Labs (ASTL) as a senior informatician, developing automated tools including 3D and time-series imaging algorithms as well as developing the necessary IT infrastructure for high-throughput image analysis. Recently he has been partnering with search vendors to drive forward a shift in how we attempt to access, aggregate and subsequently analyse our internal and external business and market information to influence strategic direction and business decisions.
Craig Bruce is a Scientific Computing Specialist at AstraZeneca. He studied Computer-Aided Chemistry at the University of Surrey before embarking on a PhD in Cheminformatics at the University of Nottingham under the supervision of Prof Jonathan Hirst. Following the completion of his PhD he moved to AstraZeneca where he works with the Computational Chemistry groups at Alderley Park. His work focuses on providing tools to aid computational and medicinal chemists across the company, such as Design Tracker, which reside on the Linux network he co-administers.
Michael Burrell is IT Manager at The Sainsbury Laboratory. He graduated with a BSc in Information Technology from the University of East Anglia and has worked extensively on creating and maintaining the computer resources at The Sainsbury Laboratory since then. Michael constructed and maintained a high-performance environment based on IBM hardware running Debian GNU Linux and utilising Platform LSF. He has extensive experience with hosting server based software in these high-performance environments.
Meiping Chang is a Senior Staff Scientist at Regeneron Pharmaceuticals. Meiping received her PhD in Biochemistry, Biophysics & Molecular Genetics from University of Colorado Health Sciences Center. She has worked in the field of Computational Biology within Pharmaceutical companies in the past decade.
Aileen Day (nee Gray) originally studied Materials Science at the University of Cambridge (BA and MSci) from 1995 until 1999, and then obtained a PhD (computer modelling zeolites) at the Chemistry department, University College London. During her postdoctoral research she adapted molecular dynamics code to calculate the lattice vibrational phonon frequencies of organic crystals. As a Materials Information Consultant at Granta Design Ltd (Cambridge, UK), she developed materials data management databases and software to store, analyse, publish and use materials test and design data. Since 2009 she has worked in the Informatics R&D team at the Royal Society of Chemistry developing RSC publications, educational projects and ChemSpider, and linking these various resources together.
David P. Dean is a Manager in Research Business Technology with Pfizer Inc. David received his BA (Chemistry) from Amherst College and MS (Biophysical Chemistry) from Yale University and has been employed at Pfizer for 20 years supporting Computational Biology and Omics Technologies as a software developer and business analyst.
Mark Earll graduated from The University of Kent at Canterbury in 1983 with an honours degree in Environmental Physical Science. After a short period working on cement and concrete additives, he joined Wyeth Research UK where he developed expertise in chiral separations and physical chemistry measurements. In 1995 Mark moved to Celltech to continue working in physical chemistry and developed interests in QSAR and data modelling. In 2001 he joined Umetrics UK as a consultant, teaching and consulting in Chemometric methods throughout Europe. In 2009 Mark joined Syngenta at Jealott’s Hill International Research Centre, where he is responsible for the metabolomics informatics platform supporting Syngenta’s seeds business.
Kirk Elder is currently CTO of WellCentive, a Population Healthcare Intelligence company that enables new business models through collaborative communities that work together to improve the quality and cost of healthcare. He has held senior technology leadership positions at various companies at the forefront of revolutionary business models. This experience covered analytics and SaaS solutions involving quality measure, risk adjustment, medical records, dictation, speech recognition, natural language processing, business intelligence, BPM and B2B solutions. Kirk is an expert in technology life-cycle management, product-to-market initiatives, and agile and open source engineering techniques.
Brian Ellenberger is currently the Manager of Software Architecture for MedQuist Inc., the world’s largest medical transcription company with a customer base of 1500 healthcare organisations and a transcription output of over 1.5 billion lines of text annually. He has over 15 years of Software Engineering experience, and eight years of experience in designing and engineering solutions for the healthcare domain. His solutions span a wide range of areas including asset management, dictation, business process management, medical records, transcription, and coding. Brian specialises in developing large-scale middleware and database architectures.
Dawn Field received her doctorate from the University of California, USA, San Diego’s Ecology, Behavior and Evolution department and completed an NSF/Sloan postdoctoral research fellowship in Molecular Evolution at the University of Oxford, UK. She has led a Molecular Evolution and Bioinformatics Group at the Centre for Ecology and Hydrology since 2000. Her research interests are in molecular evolution, bioinformatics, standards development, data sharing and policy, comparative genomics and metagenomics. She is a founding member of the Genomic Standards Consortium, the Environment Ontology, the MIBBI and the BioSharing initiative and Director of the NERC Environmental Bioinformatics Centre.
Ben Gardner is an Information and Knowledge Management Consultant providing strategic thinking and business analysis across research and development within Pfizer. He led the introduction of Enterprise 2.0 tools into Pfizer and has delivered knowledge-management frameworks that enhance collaboration and communication within and across research and development communities. More recently he has been working with information engineering colleagues to develop search capabilities and knowledge discovery solutions that combine semantic/linked data approaches with social computing solutions.
Roland C. Grafström is a tenured Professor in Biochemical Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden, since 2000, and visiting Professor, VTT Technical Research Centre of Finland, since 2008. Degree: Dr Medical Science, Karolinska Institutet, 1980. His bibliography consists of 145 research articles and 200 conference abstracts and he has a CV that lists leadership of large scientific organisations, arrangement of multiple conferences and workshops, 200 invited international lectures, and roughly 1000 hours of graduate, undergraduate and specialist training lectures. Roland received international prizes related to studies of environmental and inherited host factors that determine individual susceptibility to cancer, as well as to the development of alternative methods to animal usage. His research interests include toxicity and cancer from environmental, man-made and life style factors; molecular mechanisms underlying normal and dysregulated epithelial cell turnover; systems biology, trancriptomics, proteomics and bioinformatics for identification of predictive biomarkers; application of human tissue-based in vitro models to societal needs and replacement of animal experiments.
Niina Haiminen is a Research Staff Member of the Computational Genomics Group at IBM T.J. Watson Research Center. Dr Haiminen received her PhD in Computer Science from the University of Helsinki, Finland. Her research interests include bioinformatics, pattern discovery and data mining.
James Hardwick is a Software Engineer at Entagen and works primarily out of the Minneapolis, MN office. He began his career in 2006 working on a variety of enterprise Java projects. In 2009 he received his master’s degree in Software Engineering from the University of Minnesota. While involved in the program James fell in love with Groovy & Grails thanks in part to a class taught by Mr Michael Hugo himself. His core interests include rapidly building web-based applications utilising the Groovy/Grails technology stack and more recently developing rich user interfaces with Javascript.
Barry Hardy leads the activities of Douglas Connect, Switzerland in healthcare research and knowledge management. He is currently serving as coordinator for the OpenTox (www.opentox.org) project in predictive toxicology and the ToxBank infrastructure development project (www.toxbank.net). He is leading research activities in antimalarial drug design and toxicology for the Scientists Against Malaria project (www.scientistsagainstmalaria.net). which was developed from a pilot within the SYNERGY FP7 ICT project on knowledge-oriented collaboration. He directs the program activities of the InnovationWell and eCheminfo communities of practice, which have goals and activities aimed at improving human health and safety and developing new solutions for neglected diseases. Dr Hardy obtained his PhD in 1990 from Syracuse University working in the area of computational science. He was a National Research Fellow at the FDA Center for Biologics and Evaluation, a Hitchings-Elion Fellow at Oxford University and CEO of Virtual Environments International. He was a pioneer in the early 1990s in the development of World Wide Web technology applied to virtual scientific communities and conferences. He has developed technology solutions for internet-based conferencing, tutor-supported e-learning, laboratory automation systems, computational science and informatics, drug design and predictive toxicology. In recent years he has been increasingly active in the field of knowledge management as applied to supporting innovation, communities of practice, and collaboration. With OpenTox he is leading the development of an open, interoperable, semantic web platform whose goal is to satisfy the needs of the predictive toxicology field through the creation of applications linking resources together for data, algorithms, models and ontologies.
Lee Harland is the Founder and Chief Technical Officer of ConnectedDiscovery Ltd, a company established to promote and manage pre-competitive collaboration within the life science industry. Lee received his BSc (Biochemistry) from the University of Manchester, UK and PhD (Epigenetics and Gene Therapy) from the University of London, UK. Lee has over 13 years of experience leading knowledge management and information integration activities within major pharma. He is also the founder of SciBite.com, an open drug discovery intelligence and alerting service.
Martin Harrison is an Associate Principal Scientist at AstraZeneca, where he supports oncology discovery projects at Alderley Park as a computational chemist. His work also focuses on providing tools to aid design teams (computational, physical, synthetic, medicinal chemists and DMPK colleagues) and he uses these tools in his own projects. He developed Design Tracker and is now product owner of this global tool. In this capacity he manages the development effort and prioritises enhancement requests from the users. Previous to AstraZeneca he worked for Tularik Ltd and Protherics/Proteus Molecular Design Ltd as a computational chemist. He completed his PhD in Computational Chemistry at Manchester University under the supervision of Prof Ian Hiller in 1997.
Richard Head is the Director of Research & Development for Genomics and Pathology Services, and Director of the Genome Technology Access Center (GTAC) at Washington University School of Medicine. Prior to Washington University, he spent 14 years in pharmaceutical research. Most recently he was the leader of Computational Biology in the Inflammation & Immunology and Indications Discovery research units at Pfizer’s St. Louis Laboratories. His research has primarily focused on the application of high throughput genomic technologies, and the subsequent data interpretation, to multiple stages of drug discovery and development.
Ed Holbrook is an experienced IT professional, including five years with Astra Zeneca where he led a number of development and implementation projects, ranging barcode scanner systems to a global publication management system referencing over 50 million documents. Ed has worked as a project manager, team leader, architect, lead analyst and trainer. He has advised and assisted a number of organisations in the installation, upgrade and development of their systems, has presented at a number of national and international conferences, and has delivered a number of public training courses. Ed is currently leading the development and implementation of systems to help mobilise workers access their office-based systems via their mobile phones. When not at work, Ed enjoys taxiing his children to their various activities, running a church kids’ club, and instructing skiing at the local dry ski slope.
Jolyon Holdstock studied for a BSc in Biochemistry and Physiology at Southampton University followed by a MSc in Molecular Endocrinology at Sussex University and a PhD elucidating mechanisms regulating intracellular signalling in pituitary gonadotropes at the Royal London Hospital Medical College. Subsequently he took a postdoctoral fellowship in the Department of Experimental Pathology at Guy’s Hospital elucidating mechanisms controlling chromatin structure. Increased time spent in front of the computer forged an interest in bioinformatics and he made the switch joining the computational biology group at Oxford based startup Oxagen. Moving to another Oxfordshire located company, Oxford Gene Technology, he is currently leading the microarray probe and NGS custom bait design team.
Mike Hugo is a Senior Software Engineer at Entagen and works out of the Minneapolis, MN office. He has extensive experience with Groovy, Grails, Search and Semantic Web technologies. In addition to his expertise with these technologies he has more than seven years of enterprise Java web development, design, and technical leadership experience. He’s the author of several Grails plug-ins (including Code Coverage, Liquibase Runner, Build Info and Hibernate Stats), has been a featured author in GroovyMag and makes regular presentations at developers’ meetings. Mike holds a master’s degree in Software Engineering from the University of Minnesota and is an adjunct faculty member of the University of Minnesota Software Engineering Center.
Bernd Jagla, after receiving his PhD from the Free University Berlin, Germany in the field of bioinformatics, did a PostDoc at the Memorial Sloan-Kettering Cancer Center (MSKCC) in New York, USA in molecular biology. He then joined a bioinformatics startup company in Heidelberg, Germany developing clinically relevant workflows using an in-house workflow management system, before being recruited back to MSKCC where he pioneered some bioinformatics approaches for siRNA design and high-content high-throughput imaging. He continued his work with high-throughput confocal microscopes now integrating chemical compounds and images in the open microscopy environment (OME/OMERO) at Columbia University, New York, USA. He then became quality assurance manager for an integration platform (geWorkbench) developed at Columbia University. He is currently working as a bioinformatician at the Institut Pasteur in Paris developing KNIME nodes and workflows solving problems related to next-generation sequencing.
Nina Jeliazkova received a MSc in Computer Science from the Institute for Fine Mechanics and Optics, St. Petersburg, Russia in 1991, followed by a PhD in Computer Science (thesis ‘Novel computer methods for molecular modeling’) in 2001 in Sofia, Bulgaria, and a PostDoc at the Central Product Safety department, Procter & Gamble, Brussels, Belgium (2002–2003). Her professional career started as a software developer, first at the oil refinery Neftochim at Burgas, Bulgaria, then at the Laboratory for Mathematical Chemistry, Burgas, Bulgaria (1996–2001). She joined the Bulgarian Academy of Sciences in 1996 as a researcher and network engineer at the Network Operating Centre of the Bulgarian National Research and Education Network. She is founder and co-owner of Ideaconsult Ltd and is technical manager of the company since 2009. She participated in a number of R&D projects in Bulgaria, Belgium, and EC FP5-FP7 programs. She is an author and project leader of several open source applications for toxic hazard estimation and data and predictive model management (Toxtree (http://toxtree.sf.net). AMBIT (http://ambit.sf.net). (Q)SAR Model reporting format inventory (http://qsardb.jrc.it/qmrf/). and had a leading role in the design and implementation of the OpenTox framework.
Misha Kapushesky is the Founder and Chief Executive Officer of GeneStack Limited, a company providing a universal platform for genomics application development. Prior to this Misha was Team Leader in Functional Genomics at the European Bioinformatics Institute, where he researched, taught and developed algorithms, tools and databases for managing and analysing large-scale multiomics datasets. Misha received his BA (Mathematics & Comparative Literature) from Cornell University, USA, and PhD (Genetics) from the University of Cambridge, UK.
Richard Kidd, Informatics Manager, is an ex-chemical engineer and has worked at the RSC for many years on the underlying data and production processes behind its publications. Richard’s team developed the Project Prospect semantic enhancement of its journals, based on text mining and manual quality assurance to link together similar compounds and subject terminology, and is currently integrating publications and tools with the RSC’s public access ChemSpider database. He is currently Treasurer of the InChI Trust and is also involved in the IMI Open PHACTS project.
Frans Lawaetz is Entagen’s Chief Systems Architect working out of the Boston, MA office. He has over ten years experience in Linux, software stacks, grid computing, networking, and systems automation. Frans has a Bachelor of Arts from La Salle University.
Rob Lind has worked in the field of biological sciences since completing his BSc in Applied Biology and PhD in insect neurosciences in 1998 at the University of Bath. During his PhD, Rob worked alongside Iain Couzin in the Biological Science Department who was using computer vision techniques to better understand the collective behaviour of ants for his PhD. After joining Jealott’s Hill International Research Centre to work in insect control, Rob collaborated with Iain to build up an imaging system that could be implemented in the screening for new insecticides since 1999. This imaging system evolved and demonstrated its utility to understand the response of insects to xenobiotics and the advantages that a computer vision system offered over human observation became apparent. The application of image analysis now extends into every corner of the Syngenta business, and, in 2010, the Syngenta global network for image analysis within the company led by Rob was set up to capitalise on the cross learning and sharing of ideas between scientists. For this network to operate successfully, a common platform was needed and a freely available, flexible and open source solution to perform image analysis was chosen, namely ImageJ.
Dan MacLean is Head of Bioinformatics at The Sainsbury Laboratory, Norwich, UK. Dan received a BSc and MRes in Biological Sciences from the University of Manchester and a PhD in Plant Molecular Biology from Darwin College, University of Cambridge. Dan carried out postdoctoral research in Plant Bioinformatics at Stanford University, California, USA before returning to the UK. Dan’s areas of expertise include genomics, in particular assembly and alignment with high-throughput sequencing data, genetic polymorphism detection, homology search and automatic sequence annotation, transcriptomics (microarray and RNA-seq), statistical analysis, mathematical and systems-biology approaches to modelling and visualising data and large-scale phosphoproteomics analysis. Dan has pioneered and implemented a novel biologist-first bottom-up support model that prioritises the needs of the scientist and makes support provision flexible and scalable in the Big Data era.
Eamonn Maguire completed a BSc in Computer Science at Newcastle University, UK, followed by an MRes in Bioinformatics at the same university. He is currently the Lead Software Engineer of the ISA software suite at the University of Oxford, UK, where he is also undertaking a DPhil in Computer Science focused on visualisation of biological data and meta-data; he also contributes to the development of the BioSharing catalogue. His research interests lie in bioinformatics, software engineering, visualisation and graphical user interface design and development.
James Marsh is Postdoctoral Research Fellow in the School of Chemistry at The University of Manchester, with interests in collaborative systems, scientific visualisation and the semantic web. His current research involves modelling and visualising relationships between academic publications and related data.
Catherine Marshall is a Senior Manager and Strategic Business Partner for the Translational and Bioinformatics group at Pfizer. Her primary focus is assisting Pfizer’s Research organisation in defining and implementing technology solutions in target selection and validation and computational biology. Catherine received her BSc in Management and Computer Science from Boston College, US and MSc in Computer Science from Rensselaer Polytechnic Institute, US. Catherine has over 20 years of experience managing and leading software development teams through the entire Software Development Life Cycle, SDLC. She has experience working in the pharmaceutical, finance, energy services, and insurance industries.
Thorsten Meinl is currently working as a postdoc in the Computer Science Department at the University of Konstanz. He graduated from the University of Erlangen-Nuremberg in 2004 and received his PhD in 2010 on the topic of ‘Maximum-Score Diversity Selection’ from the University of Konstanz. His current research topics are optimisation with metaheuristics and parallel computing. He is also interested in chemoinformatics and has worked on a couple of projects with several pharma companies. He is also affiliated with KNIME.com and has been working on KNIME for more than five years.
Ted Naleid is a Senior Software engineer at Entagen’s Minneapolis, MN office. He an active contributor to the Groovy and Grails open source communities and is the author of a number of popular Grails plug-ins including the redis, build-test-data, jasypt encryption, and markdown plug-ins. He frequently speaks at conferences and user groups. Before Entagen, Ted was the Technical Architect at Bloom Health, where he built and led a team of developers through a successful acquisition by three of the largest health insurers in the country. He also has extensive experience with the Semantic Web and was one of the first developers at the semweb startup Evri in Seattle, WA.
Nguyen Nguyen is a Senior Software Engineer at Entagen and works out of the Minneapolis, MN office. He began his career in 2000 working on various technologies from Linux driver development to web application development. Nguyen holds a BS in Computer Science, and a MS in Software Engineering from the University of Minnesota.
Ketan Patel is currently a Healthcare Solutions Consultant with Oracle Health Sciences working on translational medicine solutions. Prior to this post he has led multiple teams and projects both at Pfizer and at Lilly working on translational bioinformatics in the fields of oncology, diabetes and inflammation over a nine-year period. Dr Patel holds a PhD in Bioinformatics from the University of Oxford and an MSc in Artificial Intelligence from the University of Edinburgh.
Steve Pettifer is a Senior Lecturer in Computer Science with interests in distributed systems, computer graphics, human/computer interaction and visualisation. His current research involves the application of semantic technologies to the design of user interfaces, with a particular focus on improving access to scholarly publications and biochemical data.
Simon Revell has been in the IT industry for 15 years covering a variety of technical lead, project management and consultancy roles on projects for customers in Europe, Asia and the US. In recent years he has become internationally recognised for his groundbreaking work implementing Web 2.0 tools and approaches for collaboration and information sharing for customers within an industry-leading Fortune 500 firm.
Philippe Rocca-Serra, PhD, received his doctorate in Molecular Genetics from the University of Bordeaux, France, in collaboration with the University of Oslo, Norway. Involved in data management for the last ten years (eight spent at the EMBL-EBI, UK) he has working expertise in ontology development, experimental design, curation and collaborative standards’ development. Currently Technical Project Leader at the University of Oxford, UK, he is the primary developer of the ISA-Tab format and the ISA software’s user specifications, and lead contributor to the BioSharing initiative, promoting standards’ awareness and re-use. He is also a core developer of ontology for biomedical investigation and board advisor for the identifiers.org project.
Susanna-Assunta Sansone, PhD, received her doctorate in Molecular Biology from the Imperial College, London, UK. She is a Team Leader at the University of Oxford, UK, with over ten years’ experience in project management focusing on curation, ontologies and software for data management. She has developed a significant expertise in the area of standardisation for the purpose of enabling reporting, sharing and meta-analysis of biological, biomedical and environmental studies. She has designed the ISA project and led the development of the software suite. She is a central player in the grass-roots data standardisation movement. Co-founder of the MIBBI and BioSharing initiative, she sits on the Board of several standardisation initiatives, including the Genomic Standards Consortium and the Metabolomics Standards Initiative.
Annapaola Santarsiero received her BSc in Software Engineering from the Politecnico of Milan, Italy. She is currently finalising an MSc in Communications Engineering at the same university where projects have included work in developing analysis workflows for miRNA and DNA microarray data at the Mario Negri Pharmacology Institute, Milan. She has developed the initial BioSharing catalogue and currently is a web developer in the Zoology department at the University of Oxford. Her main interests lie in web design, usability and human-computer interaction.
Ola Spjuth is a researcher at Uppsala University with main research interests in developing e-Science methods and tools for computational pharmacology and especially drug metabolism and safety assessment. He is advocating the use of high-performance computing, web-based services, and data integration to address the challenges of new high-throughput technologies, and is the deputy Director of Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX, www.uppmax.uu.se). Dr Spjuth obtained his PhD in 2010 from Uppsala University, Sweden on the topic of pharmaceutical bioinformatics. After this he did a postdoc at Karolinska Institutet, Sweden, in the field of data integration and cancer informatics. He is the author and project leader of the Bioclipse (www.bioclipse.net) project, which is a free and open source integration platform and graphical workbench for the life sciences. He is also currently serving as coordinator for the Swedish national initiative for Next Generation Sequencing storage and analysis (UPPNEX, www.uppnex.uu.se). as well as coordinating the Swedish e-Science Research Center (SeRC, www.e-science.se) in the Complex Diseases and Data Management communities.
Claus Stie Kalles0e has been working with data management and informatics in pharma research since 2000. Claus finalised his MSc (pharm) in 1997 with a thesis in synthetic medicinal chemistry and was then engaged at H. Lundbeck A/S as section head of the compound management group and in 2000 appointed Head of Department of Discovery Informatics. From 2003 to 2005 Claus also held a position as Executive Assistant to SVP of Research Dr Peter Hongaard Andersen. In 2008 Claus was appointed Chief Specialist/Director of Global Research Informatics. The informatics group at Lundbeck mainly use open source tools for their in house development and the group promotes the sharing of tools and ideas. Claus is also engaged in several pre-competitive activities. He was PM for the second round of IMI knowledge management calls leading to the current OpenPhacts project, he holds a seat in the PRISME forum and on the Board of Directors of the Pistoia Alliance. Claus also holds a Diploma in Software Development and an E-MBA from INSEAD in France.
David Stokes is Global Lead for Information Systems Consulting and Compliance at Business & Decision Life Sciences, an international Consultancy and Systems Integrator. Originally qualifying as a process control engineer in the early 1980s, he has more than 25 years’ experience in validation and compliance of information systems in the life sciences industry and is a leading participant in industry organisations such as ISPE®/GAMP. His pragmatic and cost-effective risk-based approach to applying established principles of computer systems validation to newer information systems technologies such as open source software, cloud computing, agile software development life cycles and middleware/ service oriented architecture is widely recognised, and he is a regular speaker at international conferences and has written a wide range of published papers, articles and books on the subject of information systems compliance.
Chris Taylor, PhD, received his doctorate in Population Genetics and Speciation from the University of Manchester, UK. A member of the Natural Environment Research Council’s Environmental Bioinformatics Centre based at the EMBL-EBI, UK, he is a coordinator of the MIBBI project. He has also taken various roles in a wide range of domain-specific standardisation projects, such as the Proteomics Standards Initiative.
Simon Thornber is a senior IT consultant at GlaxoSmithKline. Simon has worked in the life science industry for over 15 years, moving from Technology Development, to BioInformatics, to Cheminformatics, and then into R&D IT. He is also currently the work-group chair for the Pistoia Alliance ‘Sequence Services’ project (www.pistoiaalliance.org).
Dave Thorne is a postdoctoral research fellow in Computer Science, interested in the design of semantically rich software systems, specifically for the biosciences. He has worked for the past half-decade on modelling and visualisation (e.g. CINEMA, Ambrosia, Utopia) and now focuses his expertise on applying these techniques to the scholarly literature.
Valery Tkachenko has graduated from the Lomonosov Moscow State University, receiving his MSc in Chemistry and BSc in Computer Sciences. He is currently Chief Technology Officer of ChemSpider at the Royal Society of Chemistry. Over the course of the last 15 years he has participated in the development of a number of successful enterprise projects for large pharmaceutical companies and the public domain, including PubChem. He is the author of over 20 peer reviewed papers and book chapters.
Aristotelis Tsirigos is a research staff member of the Computational Genomics Group at IBM T.J. Watson Research Center. Dr Tsirigos received his PhD in Computer Science from the Courant Institute of New York University (with Prof Dennis Shasha). His research interests include cancer genomics, algorithms and data mining.
Filippo Utro is a postdoctoral researcher as a member of the Computational Genomics Group at IBM T.J. Watson Research Center. Dr Utro received his PhD in Mathematics and Computer Science from the University of Palermo, Italy. His research interests include algorithms and data structure, bioinformatics, pattern discovery and data mining.
Phil Verdemato is a software engineer at Thomson Reuters. He has a BSc in Biochemistry, a PhD in Biophysics and a Masters in Bioinformatics, and has spent the last ten years developing software for life sciences and financial institutions.
David Wild is Assistant Professor of Informatics and Computing at Indiana University School of Informatics. He directs the Cheminformatics Program, and leads a research group of approximately 15 students focused on large-scale data mining and aggregation of chemical and biological information. David has developed a teaching program in cheminformatics at the university, including an innovative distance education program, most recently resulting in an online repository of cheminformatics teaching materials. He has been PI or CoPI on over $1.4m of funding, and has over 30 scholarly publications. David is Editor-in-Chief (along with Chris Steinbeck at the EBI) of the Journal of Cheminformatics, and works as an editorial advisor or reviewer to many journals. He is involved in several cheminformatics organisations including being a trustee of the Chemical Structure Association Trust and a member of the American Chemical Society. David has helped organise many conferences and symposia in this field, and has recently acted as an expert witness in cheminformatics. He is also the director of Wild Ideas Consulting, a small scientific computing company specialising in informatics and cheminformatics.
Antony Williams is the VP of Strategic Development at the Royal Society of Chemistry and the original founder of ChemSpider, one of the world’s primary internet resources for chemists. He holds a BSc Hons I from the University of Liverpool and obtained his PhD from the University of London focused on Nuclear Magnetic Resonance. He held a postdoctoral position at the National Research Council in Ottawa, Canada before joining the University of Ottawa as their NMR Facility Manager. He was the NMR Technology Leader at the Eastman Kodak Company in Rochester, NY for over five years before joining Advanced Chemistry Development (ACD/Labs) where he became Chief Science Officer focusing his cheminformatics skills on structure representation, nomenclature and analytical data handling. He is known as the ChemConnector in the chemistry social network and is a blogger and active participant in Wikipedia Chemistry.
Egon Willighagen studied Chemistry at the University of Nijmegen in the Netherlands (1993–2001) with a major in chemometrics at the Department of Analytical Chemistry (Prof LMC Buydens) studying the unsupervised classification of polymorphic organic crystal structures. He continued his studies in the same group on the relation of representation of molecular knowledge and machine learning during his PhD (ISBN:978-90-9022806-8). Taking advantage of his extra-curriculur research in (open source) cheminformatics, he worked on methods to optimise the amount of information gained from pattern recognition methods in the fields of Quantitative Structure–Activity Relationships (QSAR), supervised clustering and prediction of properties of organic crystal structures, the general reduction of error introduced in exchange of chemical data, and on improving the reproducibility of data analysis in this field in general. This research was partly performed at the European Bioinformatics Institute (Prof J. Thornton) and the University of Cambridge (Prof P. Murray-Rust). After his PhD research he continued his efforts on reducing the error introduced by data aggregation and cheminformatics toolkits with postdoctoral research in Cologne (Dr C. Steinbeck), and Wageningen University and the Netherlands Metabolomics Center (Dr R. Van Ham) in the area of metabolite identification, and after that in proteochemometrics at Uppsala University (Prof J. Wikberg). After a short project in text mining for chemistry back at the University of Cambridge (Prof. P Murray-Rust), Willighagen started in 2011 a post-doc at the Institute of Environmental Medicine of the Karolinska Institute (Prof B. Fadeel, and Prof R. Grafstrom) working on applications of cheminformatic in toxicology. In January 2012 he will start a postdoc position at Maastricht University to work on the EU FP7 project Open PHACT with Dr C. Evelo. Willighagen is editorial member for two journals in the field cheminformatics and scientific computing, and member of advisory boards of various international organisations, and has been awarded for his contributions to open science in cheminformatics.
Timo Wittenberger studied Biochemistry at the Universities of Tuebingen and Tucson and received his PhD from the Center for Molecular Neurobiology at the University of Hamburg, Germany. He then joined Altana Pharma as bioinformatician and later was responsible for the research IT at the same company. In 2007 he joined Genedata, a leading bioinformatics company delivering innovative solutions for data analytics and R&D workflows, where he is managing professional services and research collaborations.